title: VIRGO: visualization of A-to-I RNA editing sites in genomic sequences.
abstract: BACKGROUND
  RNA Editing is a type of post-transcriptional modification that takes place in the eukaryotes. It alters the sequence of primary RNA transcripts by deleting, inserting or modifying residues. Several forms of RNA editing have been discovered including A-to-I, C-to-U, U-to-C and G-to-A. In recent years, the application of global approaches to the study of A-to-I editing, including high throughput sequencing, has led to important advances. However, in spite of enormous efforts, the real biological mechanism underlying this phenomenon remains unknown.
  
  
  METHODS
  In this work, we present VIRGO (http://atlas.dmi.unict.it/virgo/), a web-based tool that maps Ato-G mismatches between genomic and EST sequences as candidate A-to-I editing sites. VIRGO is built on top of a knowledge-base integrating information of genes from UCSC, EST of NCBI, SNPs, DARNED, and Next Generations Sequencing data. The tool is equipped with a user-friendly interface allowing users to analyze genomic sequences in order to identify candidate A-to-I editing sites.
  
  
  CONCLUSIONS
  VIRGO is a powerful tool allowing a systematic identification of putative A-to-I editing sites in genomic sequences. The integration of NGS data allows the computation of p-values and adjusted p-values to measure the mapped editing sites confidence. The whole knowledge base is available for download and will be continuously updated as new NGS data becomes available.
authors.affiliation: Department of Mathematics and Computer Science - University of Catania, Catania, Italy.
authors.forename: Rosario
authors.initials: R
authors.lastname: Distefano
authors.forename: Giovanni
authors.initials: G
authors.lastname: Nigita
authors.forename: Valentina
authors.initials: V
authors.lastname: Macca
authors.forename: Alessandro
authors.initials: A
authors.lastname: Laganà
authors.forename: Rosalba
authors.initials: R
authors.lastname: Giugno
authors.forename: Alfredo
authors.initials: A
authors.lastname: Pulvirenti
authors.forename: Alfredo
authors.initials: A
authors.lastname: Ferro
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D023281:Genomics; D008969:Molecular Sequence Data; D017393:RNA Editing; D012984:Software